Saturday, August 22, 2009

After speaking at length with all of you and a number of other people with an interest in the issue, we have decided that faculty furlough days will not occur on instructional days (days for which a faculty member is scheduled to give lectures, lead classes or workshops, have scheduled office hours, or have other scheduled face-to-face responsibilities for students).

The furloughs that have been necessitated by the severe University underfunding by the State are causing significant problems for faculty who have restrictions on research and service as well as increased teaching workloads; employees who have fewer days to do their work and sometimes fewer colleagues to help them; administrators who have reduced staff and budgets to accomplish their complex tasks; on top of lower salaries for everyone. Students too will suffer the effects of the underfunding--larger and fewer classes, and increased fees, as were imposed for this fall instruction period, among other burdens. In such difficult times, I believe that we must do everything we can to ensure that the students continue to receive all of their instruction. Asking the faculty to carry a full teaching load during furloughs is a large request, but in my mind is justified by the University’s paramount teaching mission. Research is permitted on furlough days, but for many faculty this extra research will not be remunerated unless they have grants in which there are funds that can be reallocated to pay for increased effort. And since furlough days are not “service days”, they can be used for outside professional activities that may be remunerated.

We understand that the furlough plan will cause hardships for the entire University family. As such, the President and the Regents are committed to do everything possible to ensure that the plan ends after 12 months.

We will continue to work closely with faculty, students, staff and administrators to find the most efficient and thoughtful way to address the problems that will arise this year. You have my pledge that we will make the University as effective and productive as we can under the current budget problems, after which we will help you all plan for better times ahead.

Best wishes,

Lawrence H. Pitts

Interim Provost and Executive Vice President

Academic Affairs

I am sure many of my colleagues will disagree with this decision by UC. The debate around campus here has basically been about whether there should be some teaching "consequences" to all the cuts being placed on faculty. I accept that it could be useful for there to be some pain and that teaching less would be a way to show that the cuts have real impact on education. But I think personally this would be a horrible political move right now. California's budget could still go down next year and there could be more cuts. UC needs as much good will as possible in Sacramento and around the state and having faculty cut teaching days does not seem to be the best maneuver.

What do other people think? I propose we slash committees, meetings, and other "service" activities like that. Many of them won't be missed by anyone.

Wednesday, August 19, 2009

A bit old here but was cleaning out my email inbox and just found a message about a cool Open Science story.

Seems Ivan Baxter and others had submitted a paper to PLoS Genetics (it is published now - see here). As described in his Ionomics Blog (yes, another omics, but we will let than slide here):

We just got the reviews back from Plos Genetics for our esb1 paper. There were many constructive suggestions and helpful suggestions, which is what we have come to expect from Plos Genetics (and why we submit many of our manuscripts there).

One of the reviewers actually came to Piims and retrieved some of the data that went into the paper to make the point that we should comment on the Mg effect of the mutation. Specifically, the reviewer pointed out that the mutation doesn't affect Mg, even though it affects Ca. They even included a figure of the data! I am posting the figure here, Blue is the mutant, and pink is the wild-type.

Go check out his post to see the figure. In the end, by putting their data out in the open, and by having a good intentioned reviewer, they got a really useful suggestion for their work ...

The Research Information Network (RIN) and the National Endowment for Science, Technology and the Arts (NESTA) are looking to fund a series of case studies which will look at what motivates researchers to work in an open way with their data, results and protocols, and whether there are advantages to working this way. The case studies will also examine the disincentives and barriers to such ‘open science’ methods. The RIN and NESTA are making available up to £15,000 for this project, which is intended to run from October 2009 until January 2010.

Expressions of interest are sought, in the form of an outline statement, on not more than a single sheet of A4, indicating the scope and rational of the proposal, the research methodology likely to be used and suggestions of case studies to be examined. The deadline is 9 September 2009. For more information visit http://www.rin.ac.uk/open-science

Tuesday, August 18, 2009

I had been growing somewhat fond of the American Society for Microbiology (ASM) recently. I had a decent time at the annual meeting. I am chair elect for Division R (Evolutionary and Genomic Microbiology) within ASM. And though their journals are not fully open access, they at least are making efforts to put material into Pubmed Central pretty rapidly. But the amount of crap I get in the mail courtesy of ASM is really astounding. And today could be the proverbial straw. I got an offer for an ASM Credit Card via Bank of America with an APR that can be raised to more than 27% with one late payment. Umm, thanks but no thanks. And note to anyone out there thinking of signing up for ASM or their meetings - get ready for a massive waste of paper when your name and address get sold to marketers and annoying junk mail. Fun fun fun.

Carl Zimmer has recently been writing about words that should be banned from scientific communication. Originally, I thought this notion was hokie but then I read his postings about it and am starting to warm to the idea. In essence he is railing against jargon. Words and phrases he thinks are to be avoided include

Breakthrough

Captive observation

Demographic leveling

Marine environment

Material properties

Morphology

Phylogenetics

When I was browsing his posting something pretty funny started to happen. Ads popped up making use of the banned terms. The best is shown in the one below:

This features an ad from Phizer for its "Big Think/ Breakthroughs" campaign to "explore medical science at the cutting edge." I guess Zimmer has not yet set up an ad blocker system which will keep out ads that use the banned terms ...

I got another bizarre phishing email with the lure being something to do with Elsevier journals. Note to any gullible people out there - if Elsevier were recruiting people to do something (e.g., write papers, be editors, etc) my guess is the request would come from an Elsevier.Com email address.

Anyway here is some of the latest:

BREAKING BOUNDRIES

The Editorial Policy and Practices Of The Elsevier Journals

1. The Editorial Board

Elsevier journals are headed by Editors and an Editorial Board Members. The Editors and Editorial Board is appointed by the Publication Committee of Elsevier Journals. Editors serve a 3-year term and Editorial Board members also serve a 3-year term. Board members are chosen based on the journal’s need for representation from a particular subject area in conjunction with the individual’s commitment to maintaining high journal standards as illustrated in objective and prompt reviews.

An Editorial Office Team is also appointed by the publication committee to directly assist the editors and editorial board members.

II. The Review Process

The Elsevier Journals editorial office policy requires each manuscript be reviewed by individuals who are highly competent and recognized in the particular field of the submitted manuscript. The editorial office contacts those reviewers that have been identified as qualified and/or recommended by the authors. Authors are also encouraged to submit in their cover letters names of individuals whom they feel are appropriate and qualified to review their manuscript. Once potential reviewers agree to read a manuscript they are given a one-week time-frame to complete the review

When the reviews are completed, a decision is made to either accept the paper or give the authors the opportunity to revise according to reviewers’ suggestions or to reject the paper based on the reviewers’ criticisms and the editors’ opinion of the paper. In some instances it is necessary to seek the opinion of other reviewers if further comment is necessary to make a final decision. When an editor has completed his decision on a manuscript, the decision letter and reviewers’ comments are sent to the author. Any questions or concerns regarding the editorial decision on any manuscript must be made directly to the Elsevier Journals editorial office. Revised manuscripts are evaluated to determine if the author(s) have adequately addressed and answered the critiques of the reviewers and editors. Depending upon this evaluation, manuscripts may be accepted, returned for further revision, or rejected. If a paper is accepted, the paper is immediately sent to the publication office and slotted for the next available issue. Elsevier journals tries to complete the review cycle in one week. This time, however, may vary depending on the amount of revision work that needs to be completed before the manuscript is acceptable.

111. Grounds for Declining a Manuscript

Elsevier Journals will decline a manuscript after it has completed the review process. Manuscripts that do not meet the standards of the journal are returned to authors with substantial comments describing the basis for the decision. Manuscripts may be rejected if it is felt that the findings are not sufficiently novel, do not provide sufficient new insights, do not contain enough new information, or are too preliminary to warrant publication.

V1. Guidelines

1. Obligations of an Editor

The editor should give unbiased consideration to all manuscripts offered for publication, judging each on its merits without regard to race, gender, religious belief, ethnic origin, citizenship, or political philosophy of the author(s).

The editor should process manuscripts promptly.

The editor has complete responsibility and authority to accept a submitted paper for publication or to reject it. The editor may confer with reviewers for an evaluation to use in making this decision.

The editor and the editorial staff should not disclose any information about a manuscript under consideration to anyone other than reviewers and potential reviewers.

The editor should respect the intellectual independence of authors.

Editorial responsibility and authority for any manuscript authored by the editor and submitted to the journal should be delegated to some other qualified person. The editor should avoid situations of real or perceived conflicts of interest. If the editor chooses to participate in an ongoing scientific debate within his journal, the editor should arrange for some other qualified person to take editorial responsibility.

The editor should avoid situations of real or perceived conflicts of interest. Such conflicts include, but are not limited to, handling papers from present and former students, from colleagues with whom the editor has recently collaborated, and from those in the same institution.

Unpublished information, arguments, or interpretations disclosed in a submitted manuscript should not be used in an editor's own research except with the consent of the author.

If the editor is presented with convincing evidence that the main substance or conclusions of a paper published in the journal are erroneous, the editor should facilitate publication of an appropriate paper pointing out the error and, if possible, correcting it.

2. Obligations of Reviewers of Manuscripts

Inasmuch as the reviewing of manuscripts is an essential step in the publication process, every scientist has an obligation to do a fair share of reviewing.

A chosen reviewer who feels inadequately qualified or lacks the time to judge the research reported in a manuscript should return it promptly to the editor

A reviewer of a manuscript should judge objectively the quality of the manuscript and respect the intellectual independence of the authors. In no case is personal criticism appropriate.

A reviewer should be sensitive even to the appearance of a conflict of interest when the manuscript under review is closely related to the reviewer's work in progress or published. If in doubt, the reviewer should return the manuscript promptly without review, advising the editor of the conflict of interest or bias.

A reviewer should not evaluate a manuscript authored or co-authored by a person with whom the reviewer has a personal or professional connection if the relationship would bias judgment of the manuscript.

A reviewer should treat a manuscript sent for review as a confidential document. It should neither be shown to nor discussed with others except, in special cases, to persons from whom specific advice may be sought; in that event, the identities of those consulted should be disclosed to the editor.

Reviewers should explain and support their judgments adequately so that editors and authors may understand the basis of their comments. Any statement that an observation, derivation, or argument had been previously reported should be accompanied by the relevant citation.

A reviewer should be alert to failure of authors to cite relevant work by other scientists. A reviewer should call to the editor's attention any substantial similarity between the manuscript under consideration and any published paper or any manuscript submitted concurrently to another journal.

Reviewers should not use or disclose unpublished information, arguments, or interpretations contained in a manuscript under consideration, except with the consent of the author

Reviewers should respond promptly, usually within one week of receipt of a manuscript. If reviewers need more time, they contact the editor promptly so that authors can be kept informed and, if necessary, assign alternate reviewers

There is a letter attached to it and also the procedures on how to fill the form

We would appreciate if you contact us as soon as possible because we are updating our data sheet for reviewers and editors which we want to upload in our website soonest. Thank you for your co-operation. Please reply to board.elsevier@gmail.com

Please note that you are to pay $100, for more details please read the letter attached below.

Best regards

Chief editor

------------------------------------------------------------

Then the form asks for:

Please read the letter carefully before filling the form.Before filling this form you have to accept the conditions stated regarding the payment and on our own part we are to pay you for each work sent to you.Payment is done only when you are accepted to become a member.

Name of Editor Date of Birth Area of Specialization Degree No. of Articles Published

Name of Reviewer Date of Birth Area of Specialization Degree No. of Articles Published

And a separate PDF says

Dear colleague,Elsevier publishes the largest journals online which is a close accesssystem. Each year we organize a routine test for all our reviewersand editors to ascertain their level of research in the reviewing andediting of articles before publication. We would like to know if you areinterested in serving as a member of our reviewing and editorialboard. You are required to pay $100 to enable us include yourname on our website. Successful candidate will be paid $30 perpage of manuscript given to review or edit. Please fill the formattached.

For those interested in so-called "third generation" DNA sequencing systems, this week has had some buzz with the release of a publication in Nature Biotechnology reporting the sequencing and analysis of a human genome using a Helicos Heliscope sequencer. In this paper Stephen Quake and colleagues generated short read sequences from Quake's DNA using this machine and then analyzed them by comparing them to reference human genomes.

Certainly, what they did was cool. And the use of the Helicos equipment is a good thing for that company and it's development of single molecule sequencing. And given the "race" if you want to call it that for the $1000 genome, it is thus not surprising that this paper received a lot of coverage from all sorts of angles because they claim it involved the cheapest sequencing of a human genome yet achieved.

So first I want to commend Quake and Helicos for an important step in third generation sequencing. Quake mind you is one guy who is constantly inventing cool new techniques of great use in genomics and biology and he is always worth checking out.

But in this case, there are some aspects of what they claim they achieved here that are very off putting. In particular, I am concerned with the supposed "democratization of sequencing" that they think this project embodies (e.g., see some of the quotes in this). The basis for their concluding that democratization has happened here is that they believe this sequencing (of Quake's genome) was done at lower cost and with less effort than previous human genome sequencing efforts. To back this up they make a table (Supplemental Table 1) detailing estimates of these values for 8 human genome papers (the original Lander et al and Venter et al ones, as well as Watson's genome, etc) that is meant to represent some of this information).

In essence Quake et al are doing the following math (my formula, not theirs, but their discussions imply basically this)

That is, with more sequence, less effort, or less cost, the more democratized sequencing is. Sounds fine in some ways. Except when you look at the details.

For example consider the cost (C) of the sequencing. They report that the cost for the sequencing was < $50,000. But this number is misleading since, for example, they do not include any aspect of the cost of actually buying and setting up the machine. For more detail on the flaws in the cost calculation and for more detail on the whole story see Times Onlineand Dan Macarthur at Genetic Future and GenomeWeb).

However, more disconcerting to me is what they do with the rest of the implied calculation.

For example, they treat all the projects in essence as though they are equal in terms of total number of bases sequenced (B) because I guess after all, all were sequencing human genomes. But this is not fair since the depth of sequencing and the quality of sequencing varies between the projects and more recent projects, such as theirs, make use of the data from prior projects, which allows them to gather less data (e.g., in their paper here they assemble the genome by tiling the reads against reference genomes, thus allowing them to do lower coverage than would be required for denovo assemblies of genomes).

But even worse - the way they calculate effort required (E) is flabbergasting.

They seem to infer this in two ways. First, they make use of the number of runs of the machine that are required. They apparently used four runs while they claim that the use of second generation sequencing methods required many more runs. And many have been questioning this claim (e.g., see Chad Nusbaum's quotes in the GenomeWeb article).

It is the second way that they infer effort that is perhaps the most annoying. They infer this from number of authors on the papers describing the sequencing of these human genomes (e.g., In Supplemental Table 1 they say "number of authors" is "an estimate of labor.") And the big thing for Quake et al is that there are only three authors on their paper and dozens to hundreds on other human genome papers. Based on this lower number of authors they conclude that their work required less effort and discuss this as evidence for further democratization of sequencing.

Now suppose we gloss over that there is no way to infer amount of effort by number of authors (e.g., letters to the editor, which usually do not require a lot of effort, can sometimes have hundreds of authors while Origin of Species had but one author and was, shall we say, a lot of work). Even worse to me is that they are trying to compare their paper which is focused almost entirely on the technical aspects of the sequencing with other papers that spend much more effort on studying and discussing what the genomes might mean. For example the Venter/Celera and the public human genome papers are complex detailed volumes with analysis of everything you could think of. To compare the effort required to do this with the effort required to do what they did in the Quake paper which was pretty much assembly and analysis of SNPs is inappropriate and actually offensive.

Given the number of areas that they have oversold how their project has reduced effort and cost for sequencing a human genome and how this implies democratization, I am giving Quake and Helicos my coveted "Overselling genomics award". Again, not that what they did was not cool or interesting, but by overselling it, it detracts from everything they achieved.

Saturday, August 08, 2009

In this, they overlay onto a somewhat strange Tree of Life, the images used for various book publishers and what types of organisms they use. They say that this represents a fair amount of biodiversity, but really only because they draw the tree in a skewed manner. Basically, there are animals and plants in the logos and the way they draw the tree makes this look like it is a lot of biodiversity ... but really it is a small component compared to the whole tree of life. I also like that they put robots on the insect branch and they have mythology as a VERY deep branch in the tree.

The Journal of Computational Biology and Bioinformatics Research (JCBBR)is a multidisciplinary peer-reviewed journal published monthly by AcademicJournals (www.academicjournals.org/JCBBR). JCBBR is dedicated toincreasing the depth of research across all areas of this subject.

We invite you to submit your manuscript(s) to jcbbr.journal@gmail.com forpublication in the Maiden Issue (October 2009). Our objective is to informauthors of the decision on their manuscript(s) within four weeks ofsubmission. Following acceptance, a paper will normally be published inthe next issue. Instruction for authors and other details are available onour website; http://www.academicjournals.org/JCBBR/Instruction.htm

JCBBR is an Open Access Journal

One key request of researchers across the world is unrestricted access toresearch publications. Open access gives a worldwide audience larger thanthat of any subscription-based journal ad thus increases the visibilityand impact of published work. It also enhances indexing, retrieval powerand eliminates the need for permissions to reproduce and distributecontent. JCBBR is fully committed to the Open Access Initiative and willprovide free access to all articles as soon as they are published.

The engineer will work in an interdisciplinary research group of evolutionary biologists, ecologists, and statisticians. Applicants should have substantial experience with genome-scale bioinformatics, including comparative genomics, analysis of protein families, multiple sequence alignment, and phylogenetic analyses. Familiarity with SQL, Perl/Python, and standard bioinformatics tools are essential. Typical responsibilities for this position may include designing and managing an in-house MySQL database of metagenomic sequence data; running BLAST, HMMER, and AMPHORA on the Global Ocean Survey and other large metagenomic data sets; identifying OTUs (operational taxanomic units) based on 16S rRNA or proteins; writing Perl scripts to query databases, process data, or run simulations; distributing data, scripts, and information to project members on all three campuses. Strong project management skills are essential.

We will offer a generous salary and benefits commensurate with experience. The position is available immediately, and the initial appointment will be for one year. The engineer would ideally be located at UC Davis, although other arrangements will be considered.

and consist of (1) a cover letter describing your interest in the position, (2) the names and contact information for three references, (3) a curriculum vita (including publications). Applications will be reviewed upon receipt, until the position is filled.

This piece is worth reading because it contains some critical ideas and wisdom which has been missing in discussions of the fight against cancer.

First, Watson discusses the critical importance of basic science and says that when he expressed this importance to the National Cancer Institute advisory board many years ago, he was eventually booted off.

Second, he discusses how we have only recently begun to understand the basic biology of cancer (he also mentions how the human genome project has helped in this). The genome project will, he says, allow for the determination of most/all of the major genetic changes that occur in cancer cells.

Third, he discusses some limitations of the FDA drug approval process that limit the ability to test combinations of drugs which Watson believes will be needed in the fight against cancer.

Fourth he suggests that the National Cancer Institute should help support small biotech companies in the development of new drugs since venture capital has dried up for such endeavors.

As usual, Watson would not be Watson if he did not say something potentially controversial. In this, the most controversial thing is probably how he discusses that the National Cancer Institute has become a "a largely rudderless ship in dire need of a bold captain who will settle only for total victory. " Now, I do not have any opinion about this since I have not followed NCI or its leadership. But it is certainly worth considering Watson's opinion here.

In the end, Watson says the time is now to reinvigorate the "War on Cancer." Despite misgivings about many things he has been up to recently, I found myself agreeing with almost everything he said in this piece. Again, definitely worth a read.

In the article Natasha Singer reports on how Wyeth commissioned the writing by a communication firm of a series of "draft" articles that were then published under the names of various medical professionals. It seems from the article that in some if not many cases the articles were in essence written by this company and then names of authors were placed on the papers which were then submitted to various journals and were published (they were generally review papers, and shockingly supported the use of Wyeth manufactured products).

The issues here are as always complex. But in the end, the articles did not disclose the role Wyeth played in paying for the writing of drafts and/or nearly complete forms of the papers and certainly should have. For more detail, read the Times article.

Interestingly, the documents that helped uncover the full details of the practice were obtained after a "a request in court from PLoS Medicine, a medical journal from the Public Library of Science, and The New York Times." For more detail on this see the PLoS Medicine blog here. Kudos to PLoS Medicine for getting involved in this and for pushing hard for more disclosure in medical publishing.

All I can say is the practice of ghostwriting medical and scientific articles should stop. Getting help with editing a paper is one thing. But putting your name on a paper conceived of and written by someone else is unacceptable.

Tuesday, August 04, 2009

Just got pointed to this site by the author ... MelTells.Com has some online books for kids some of which have a sciency theme to them. All of them seem to have some dental connection, though not all in the same way. I have only looked at the bacteria one and it is not bad. Even though I have not looked at the others, since they are free, I am posting this bit here.

Monday, August 03, 2009

Well, I was talking with some people recently about someone who had a bad experience giving their first talk at a scientific conference. And so I said - you think that is bad - how about this? And I told them the story below. But before telling the story I am asking here for others to post comments about the worst thing that has happened to you during a talk at a scientific conference/meeting. Please fire away.

OK - so my talk. It was 1995. The SSE (Society of the Study of Evolution) meeting was in Montreal. And somehow I was going. I am not sure anymore how I ended up registering for the meeting. I do remember other evo-grad students who were or had been at Stanford like David Pollock, Joanna Mountain, maybe David Goldstein, maybe Sally Otto, Sarah Cohen, and a few others were going. And so I registered, got accepted to give a talk on the "Evolution of RecA" and made plane reservations to get to Montreal.

I arrived the night before my talk, found my dorm room on the McGill campus, and then went wandering around town for the Jazz Festival which was going on that night. After staying out pretty late, I got back to my room and had a bit of a panic attack when I looked at the schedule and found that the session in which I was talking started at 8:30 in the morning the next day and I did not have an alarm clock, nor was there one in my room. (I note, fortunately I was using real slides and could not spend the night modifying my talk in the way I do now with Keynote/PPT). Anyway - I pretty much knew I would sleep late without some work and so I made some notes with my room # and a plea to others to bang on my door if they could by 6:30 or 7 AM and I slipped these under the other doors in the hall. Fortunately in some ways, I barely slept b/c I was so scared of missing my first talk.

So at 6:30 AM or so I headed out to the conference area. I think I got some coffee and then headed to the room where my talk was to be. Nobody was even there so I wandered around for a bit and came back and the projectionist was there getting the room set up. When I said I was one of the speakers - he said "Are you planning on doing any side by side slides where you need two projectors?" Well, I had not thought of doing this, but now that he mentioned it, it sounded perfect b/c the main point of my talk was that the phylogenetic trees of RecA and rRNA were very similar to each other (see my 1995 J. Mol. Evol. paper on the topic here), supporting earlier suggestions by Lloyd and Sharp that RecA was a potentially useful phylogenetic marker. So I said "sure" and proceeded to load up two slide carousels for my talk. We checked them out and all looked good.

As the room started to fill up (I recall there were a lot of people interested in the "Molecular Evolution" session I was in) I decided to go grab a seat (in the far back on an aisle - I was a lurker even before blogging from meetings) and try to relax. I think I was the fourth talk and while speaker #3 (Michael Purugganan) was getting started I got nervous about the side by side slides so I went over to ask the projectionist if all was OK and he said it was. Alas, someone had grabbed my seat when I was up. I saw a table in the back back of the room with some misc. fliers on it so I went there to sit down for a few minutes and try to relax. And here was the trouble.

The table was also being used to hold some pitchers of water for people. And alas, someone had just spilled an entire pitcher of water on the table and I did not notice. I sat in the puddle. And there I was, in my tan shorts, now dripping wet. Minutes before my first talk. Looking like I had gotten a bit too nervous. Underwear showing through. As I desperately looked around to borrow a sweatshirt from someone to tie around my waist, the chair said "And our next speaker is Jonathan Eisen ...". Holy Crap. I was on.

So I went up there and I had thought to myself to crack a joke about just getting in from a swim. Or something. But as I still do, I entered another zone for my talk and forget everything but the talk. And so - there I was - dripping wet in my see through shorts - turning around and pointing to the screen talking about RecA as though all was fine.

Only when I was done with the talk did I re-remember that I was basically doing a "wet-shorts" contest for all in the audience. Yay. I can say truthfully that when I start to worry about things going wrong in talks, I remember this one and say "well, it could be worse ..."